On Wed, May 28, 2014 at 1:07 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir
>
> "Open your com_solvated.pdb file. Identify the mask which denote the
> ligand.
> Suppose residue mask is 556 and if you open the minimized pdb you can
> identify some crucial residues such as X1, X2 take out their atom mask.
>
> In the print residue put like this "556,X1,X2"
>
>
> Say for example you ligand mask is 905 and your crucial amino acid residues
> are 902 and 903. Then in print residue put like this "905,902,903"
> Thats it."
>
>
> As per your suggestion to go through com_solvated.pdb file , I have not
> generated com_solvted.pdb file. Moreover in the totutorial its saying to
> select residue from comlex.prmtop file.
>
> I did go through the complex.pdb file but I am not getting which residue to
> slect.
>
>
> Kindly guide me as to how to go ahead with residue selection.
>
Write PDB file from your complex prmtop and an inpcrd or a restart file
(either ambpdb or cpptraj will do this for you). Go through that PDB and
look at the residues you want to obtain pairwise energies for. Add those
residues to print_res.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researche
r
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Received on Wed May 28 2014 - 05:30:02 PDT
